Results were also hurt by weaker than expected sales of Pfizer's Prevnar vaccine and Lipitor cholesterol fighter, which has been facing cheaper generics since late last year.

The largest U.S. drugmaker earned $3.21 billion, or 43 cents per share, in the third quarter. That compared with $3.74 billion, or 48 cents per share, in the year-earlier period, when the company recorded a $1.3 billion gain on the sale of its Capsugel business.

Excluding special items, Pfizer earned 53 cents per share. Analysts on average had expected 53 cents, according to Thomson Reuters I/B/E/S.